Single cell type - CSTA - The Human Protein Atlas

GENERAL INFORMATIONⁱ General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.
Gene nameⁱ Official gene symbol, which is typically a short form of the gene name, according to HGNC.	CSTA
Gene descriptionⁱ Full gene name according to HGNC.	Cystatin A
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes Disease related genes Human disease related genes Plasma proteins
Predicted locationⁱ All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions. Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached. Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s). The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location. Read more	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	2

HUMAN PROTEIN ATLAS INFORMATIONⁱ Summary of RNA expression and protein localization based on data generated within the Human Protein Atlas project.
Single cell type expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Squamous epithelial cells - Keratinization (mainly)
Single cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Cell type enhanced (Squamous epithelial cells, Basal respiratory cells, monocytes, Club cells, Kupffer cells)
Immune cell specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Group enriched (classical monocyte, myeloid DC, intermediate monocyte, neutrophil, non-classical monocyte)
Immune cell distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in many
Cell line specificityⁱ RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines. Read more	Cell line enhanced (HBEC3-KT, hTCEpi, THP-1, U-698, U-937)
Cell line distributionⁱ RNA distribution category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into five different categories (detected in all, detected in many, detected in some, detected in single and not detected) according to their pattern of detected RNA expression across the panel of cell lines. Read more	Detected in many
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); a Human Protein Atlas antibody- or RNA based score (HPA evidence); and evidence based on PeptideAtlas (MS evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable. Read more	Evidence at protein level

SINGLE CELL TYPESⁱ A summary of single cell RNA (nTPM) from all single cell types. Color-coding is based on cell type groups, each consisting of cell types with functional features in common.
Single cell types Group Expression Alphabetical RNA single cell type specificity: Cell type enhanced (Squamous epithelial cells, Basal respiratory cells, monocytes, Club cells, Kupffer cells)

SINGLE CELL TISSUES OVERVIEWⁱ An overview of all tissues where single cell type expression has been analyzed. Each tissue name and corresponding UMAP plot is clickable and redirects to the selected tissue.
Adipose tissue Bone marrow Brain Breast Bronchus Colon Endometrium Esophagus Eye Heart muscle Kidney Liver Lung Lymph node Ovary Pancreas Placenta Prostate Rectum Skeletal muscle Skin Small intestine Spleen Stomach Testis

EXPRESSION CLUSTERING & CORRELATIONⁱ

CSTA is part of cluster 61 Squamous epithelial cells - Keratinization with confidenceⁱ 1
176 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell type RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data. Read more	Clusterⁱ ID of the expression cluster of the neighboring gene. Read more
SERPINB13	Serpin family B member 13	0.9041	61
ADH7	Alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	0.8893	61
SPRR2A	Small proline rich protein 2A	0.8763	61
KRT6A	Keratin 6A	0.8633	61
TMEM79	Transmembrane protein 79	0.8486	61
CLCA2	Chloride channel accessory 2	0.8463	61
KRT6B	Keratin 6B	0.8447	61
RHCG	Rh family C glycoprotein	0.8154	61
SPRR3	Small proline rich protein 3	0.8154	61
EPHX3	Epoxide hydrolase 3	0.8132	61
SPINK5	Serine peptidase inhibitor Kazal type 5	0.8078	61
PAX9	Paired box 9	0.8075	61
PGD	Phosphogluconate dehydrogenase	0.8057	61
KRT4	Keratin 4	0.8026	61
MUC21	Mucin 21, cell surface associated	0.7997	61

SINGLE CELL TISSUESⁱ Single cell RNA levels of annotated cell type clusters are shown separately for each analyzed tissue. For easier navigation across tissues, use the above Single cell tissue overview, where each tissue name and UMAP plot is clickable and redirects to the selected tissue, alternatively the grey browser on the left side of the window. Barchart shows nTPM levels in each annotated cluster of single cells. To the left, a UMAP plot illustrates the RNA expression profile. The tissue name and plots are clickable and redirect to a more detailed interactive page. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. Please note that the same cell type may be found in several clusters.
Cluster Expression Alphabetical Adipose tissue
Cluster Expression Alphabetical Bone marrow
Cluster Expression Alphabetical Brain
Cluster Expression Alphabetical Breast
Cluster Expression Alphabetical Bronchus
Cluster Expression Alphabetical Colon
Cluster Expression Alphabetical Endometrium
Cluster Expression Alphabetical Esophagus
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Lymph node
Cluster Expression Alphabetical Ovary
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skeletal muscle
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Spleen
Cluster Expression Alphabetical Stomach
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ

Organ

Expression

Alphabetical

Adipocytes	1.1 nTPM
Breast	1.9 nTPM
Adipose tissue	0.3 nTPM

Alveolar cells type 1	6.4 nTPM
Lung	6.4 nTPM

Alveolar cells type 2	19.8 nTPM
Lung	19.8 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	5.0 nTPM
Colon	20.8 nTPM
PBMC	18.6 nTPM
Liver	6.0 nTPM
Breast	2.6 nTPM
Lymph node	1.5 nTPM
Adipose tissue	0.5 nTPM
Spleen	0.3 nTPM
Kidney	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM

Basal squamous epithelial cells	117.8 nTPM
Esophagus	117.8 nTPM

Dendritic cells	7.4 nTPM
PBMC	20.0 nTPM
Breast	1.8 nTPM
Adipose tissue	0.4 nTPM

Endothelial cells	3.0 nTPM
Esophagus	11.3 nTPM
Lung	6.2 nTPM
Placenta	6.2 nTPM
Liver	5.5 nTPM
Prostate	4.3 nTPM
Skin	4.3 nTPM
Breast	1.8 nTPM
Skeletal muscle	0.8 nTPM
Testis	0.6 nTPM
Heart muscle	0.1 nTPM
Endometrium	0.1 nTPM
Eye	0.0 nTPM
Pancreas	0.0 nTPM
Ovary	0.0 nTPM

Fibroblasts	13.6 nTPM
Ovary	43.8 nTPM
Lung	27.9 nTPM
Breast	22.1 nTPM
Esophagus	12.6 nTPM
Placenta	9.9 nTPM
Skin	7.7 nTPM
Stomach	7.4 nTPM
Skeletal muscle	6.3 nTPM
Adipose tissue	5.6 nTPM
Prostate	3.8 nTPM
Heart muscle	2.8 nTPM

Intestinal goblet cells	0.5 nTPM
Rectum	0.8 nTPM
Colon	0.7 nTPM
Small intestine	0.0 nTPM

Macrophages	243.7 nTPM
Testis	453.8 nTPM
Kidney	440.1 nTPM
Skeletal muscle	412.5 nTPM
Stomach	345.7 nTPM
Lung	336.8 nTPM
Spleen	290.3 nTPM
Adipose tissue	230.2 nTPM
Pancreas	227.2 nTPM
Bone marrow	213.7 nTPM
Endometrium	192.0 nTPM
Ovary	128.6 nTPM
Prostate	114.6 nTPM
PBMC	109.1 nTPM
Esophagus	89.7 nTPM
Breast	71.1 nTPM

Paneth cells	1.5 nTPM
Colon	3.3 nTPM
Rectum	1.2 nTPM
Small intestine	0.0 nTPM

Plasma cells	2.8 nTPM
Esophagus	12.3 nTPM
Adipose tissue	1.9 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Respiratory ciliated cells	115.7 nTPM
Bronchus	197.9 nTPM
Lung	33.5 nTPM

Smooth muscle cells	24.3 nTPM
Bronchus	165.8 nTPM
Pancreas	68.8 nTPM
Esophagus	17.0 nTPM
Prostate	9.1 nTPM
Skin	3.8 nTPM
Ovary	0.8 nTPM
Skeletal muscle	0.7 nTPM
Breast	0.5 nTPM
Adipose tissue	0.2 nTPM
Endometrium	0.1 nTPM
Heart muscle	0.0 nTPM

Cytotrophoblasts	230.6 nTPM
Placenta	230.6 nTPM

T-cells	4.9 nTPM
Lung	31.9 nTPM
PBMC	21.8 nTPM
Esophagus	13.1 nTPM
Skin	6.0 nTPM
Liver	5.6 nTPM
Breast	1.5 nTPM
Spleen	1.0 nTPM
Skeletal muscle	0.8 nTPM
Adipose tissue	0.4 nTPM
Bone marrow	0.3 nTPM
Stomach	0.1 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
Prostate	0.0 nTPM
Endometrium	0.0 nTPM
Ovary	0.0 nTPM
Lymph node	0.0 nTPM

Undifferentiated cells	2.0 nTPM
Colon	3.3 nTPM
Rectum	2.6 nTPM
Small intestine	0.0 nTPM

Adipose tissue

Bone marrow

Brain

Breast

Bronchus

Colon

Endometrium

Esophagus

Eye

Heart muscle

Kidney

Liver

Lung

Lymph node

Ovary

Pancreas

Placenta

Prostate

Rectum

Skeletal muscle

Skin

Small intestine

Spleen

Stomach

Testis

PBMC